sarscov2_sequencing_reports
pipes/WDL/workflows/sarscov2_sequencing_reports.wdl

WORKFLOW sarscov2_sequencing_reports

File Path pipes/WDL/workflows/sarscov2_sequencing_reports.wdl
WDL Version 1.0
Type workflow

Imports

Namespace Path
sarscov2 ../tasks/tasks_sarscov2.wdl
utils ../tasks/tasks_utils.wdl

Workflow: sarscov2_sequencing_reports

Produce per-state and per-collaborator weekly reports of SARS-CoV-2 surveillance data.

Inputs

Name Type Description Default
assembly_stats_tsvs Array[File] - -
max_date String? - -
timezone String? - -
collab_ids_tsv File? - -
min_date String? - -
min_unambig Int? - -
voc_list String? - -
voi_list String? - -
6 optional inputs with default values

Outputs

Name Type Expression
assembly_stats_cumulative_tsv File tsv_join.out_tsv
sequencing_reports_pdfs Array[File] sequencing_report.reports
sequencing_reports_xlsxs Array[File] sequencing_report.sheets
sequencing_reports_zip File sequencing_report.all_zip
sequencing_report_tsv File sequencing_report.all_tsv
sequence_report_date String report_date

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS today ↗

No explicit input mappings

CALL TASKS tsv_join ↗

Input Mappings (4)
Input Value
input_tsvs assembly_stats_tsvs
id_col 'sample'
out_basename 'assembly_stats-cumulative-~{report_date}'
prefer_first false

CALL TASKS sequencing_report ↗

Input Mappings (2)
Input Value
assembly_stats_tsv tsv_join.out_tsv
max_date report_date

Images

Container images used by tasks in this workflow:

🐳 viral-baseimage

quay.io/broadinstitute/viral-baseimage:0.3.0

Used by 1 task:
  • today
🐳 viral-core

quay.io/broadinstitute/viral-core:2.5.1

Used by 1 task:
  • tsv_join
🐳 Parameterized Image
⚙️ Parameterized

Configured via input:
docker

Used by 1 task:
  • sequencing_report
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sarscov2_sequencing_reports - Workflow Graph

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sarscov2_sequencing_reports - WDL Source Code

version 1.0

import "../tasks/tasks_sarscov2.wdl" as sarscov2
import "../tasks/tasks_utils.wdl" as utils

workflow sarscov2_sequencing_reports {
    meta {
        description: "Produce per-state and per-collaborator weekly reports of SARS-CoV-2 surveillance data."
    }

    input {
        Array[File] assembly_stats_tsvs
        String?     max_date
    }

    call utils.today

    String report_date = select_first([max_date, today.date])

    call utils.tsv_join {
        input:
            input_tsvs   = assembly_stats_tsvs,
            id_col       = 'sample',
            out_basename = 'assembly_stats-cumulative-~{report_date}',
            prefer_first = false  # always prefer later sequencing results over earlier ones
    }

    call sarscov2.sequencing_report {
        input:
            assembly_stats_tsv = tsv_join.out_tsv,
            max_date           = report_date
    }

    output {
        File        assembly_stats_cumulative_tsv = tsv_join.out_tsv
        Array[File] sequencing_reports_pdfs       = sequencing_report.reports
        Array[File] sequencing_reports_xlsxs      = sequencing_report.sheets
        File        sequencing_reports_zip        = sequencing_report.all_zip
        File        sequencing_report_tsv         = sequencing_report.all_tsv
        String      sequence_report_date          = report_date
    }
}